Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF4164 Psest_4237 succinate-semialdehyde dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__psRCH2:GFF4164 Length = 482 Score = 212 bits (540), Expect = 2e-59 Identities = 155/470 (32%), Positives = 236/470 (50%), Gaps = 22/470 (4%) Query: 3 ELFIDGAWVDG-AGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDA 61 + +IDGAW+D +G + NP T E + A + RA+ +A RA AW L Sbjct: 12 QAYIDGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERALPAWRDLTAKE 71 Query: 62 RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK- 120 R ++R+ LL+E ++ L ++ E GKPL EA+ E+A A+ ++ G+ Sbjct: 72 RSQKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTI 131 Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 D ++ +P GV A P+NFP + PAL AG T+V KP+ P A A Sbjct: 132 PGHQKDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALA 191 Query: 181 TVEIWRDAGLPAGVLNLVQGEK-DTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 VE+ AG+P GVL++V G D G L + ++ + FTGS++ G L +Q P I Sbjct: 192 MVELAERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAKLMEQCA--PGI 249 Query: 240 -VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298 ++LE+GGN P +V + D+D AV A+QS + +AGQ C C RI V G + D F + Sbjct: 250 KKVSLELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDGVY-DTFAEK 308 Query: 299 LADVASKITASVFDADPQPFMGAVISARAASRL-------VAAQARLVGLGASPIIEMKQ 351 +K+ + +G +I RAA+++ VA ARLV G + + Sbjct: 309 FQAAVAKLRVG-NGLEEGTDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQAHALGGSY 367 Query: 352 RDPALGFVNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLAD 411 +P + +++V + ++ EE FGPLA + R+ D DAIA+ANDT FGL++ A Sbjct: 368 FEPTV------LVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYAR 421 Query: 412 DEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461 D A+ G+V N ++ APFGG SG R + Y + Sbjct: 422 DLGRVFRVAEALEYGMVGINTGLI-STEVAPFGGVKSSGLGREGSKYGIE 470 Lambda K H 0.320 0.134 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 484 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 482 Length adjustment: 34 Effective length of query: 453 Effective length of database: 448 Effective search space: 202944 Effective search space used: 202944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory